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German P. Barletta pgbarletta

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pgbarletta / gcc_output
Created March 21, 2018 22:28
gcc_output
tes.c:6:25: error: initializer element is not constant
CHFL_TRAJECTORY* file = chfl_trajectory_open("1M14.pdb", 'r');
^~~~~~~~~~~~~~~~~~~~
tes.c:7:21: error: initializer element is not constant
CHFL_FRAME* frame = chfl_frame();
^~~~~~~~~~
tes.c:8:1: warning: data definition has no type or storage class
chfl_trajectory_read(file, frame);
^~~~~~~~~~~~~~~~~~~~
tes.c:8:1: warning: type defaults to ‘int’ in declaration of ‘chfl_trajectory_read’ [-Wimplicit-int]
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pgbarletta / piola.cpp
Created June 8, 2018 15:26
#include <iostream>
#include <chemfiles.hpp>
int main() {
chemfiles::Trajectory in_trj("/home/german/labo/18/lbp/run/4xcp/pca/full_avg_4xcp.pdb");
std::cout << " " << in_trj.nsteps() << '\n';
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pgbarletta / 99999_4xcp.pdb
Created June 8, 2018 16:02
ATOM 1 N PHE 1 36.629 31.298 16.713 1.00 0.00 N
ATOM 2 H1 PHE 1 37.504 31.800 16.668 1.00 0.00 H
ATOM 3 H2 PHE 1 36.681 30.534 16.055 1.00 0.00 H
ATOM 4 H3 PHE 1 35.908 31.927 16.391 1.00 0.00 H
ATOM 5 CA PHE 1 36.256 30.646 17.997 1.00 0.00 C
ATOM 6 HA PHE 1 36.986 29.855 18.172 1.00 0.00 H
ATOM 7 CB PHE 1 36.397 31.604 19.188 1.00 0.00 C
ATOM 8 HB2 PHE 1 37.410 31.821 19.526 1.00 0.00 H
ATOM 9 HB3 PHE 1 35.896 32.527 18.895 1.00 0.00 H
ATOM 10 CG PHE 1 35.788 31.068 20.432 1.00 0.00 C
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pgbarletta / nvcc_errors.txt
Created August 26, 2018 16:01
/usr/include/CGAL/Triangulation_3.h:2294:1: error: prototype for ‘CGAL::Triangulation_3<GT, Tds, Lock_data_structure>::Triangle CGAL::Triangulation_3<GT, Tds, Lock_data_structure>::triangle(typename CGAL::Default::Get<typename CGAL::Default::Get<Tds_, CGAL::Triangulation_data_structure_3<CGAL::Triangulation_vertex_base_3<GT>, CGAL::Triangulation_cell_base_3<GT> > >::type, CGAL::Triangulation_data_structure_3<CGAL::Triangulation_vertex_base_3<GT>, CGAL::Triangulation_cell_base_3<GT> > >::type::Cell_handle, int) const’ does not match any in class ‘CGAL::Triangulation_3<GT, Tds, Lock_data_structure>’
triangle(const Cell_handle c, int i) const
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/CGAL/Triangulation_3.h:772:10: error: candidates are: CGAL::Triangulation_3<GT, Tds, Lock_data_structure>::Triangle CGAL::Triangulation_3<GT, Tds, Lock_data_structure>::triangle(const Facet&) const
Triangle triangle(const Facet & f) const
^~~~~~~~
/usr/include/CGAL/Triangulation_3.h:770:10: error: CG
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pgbarletta / config.h
Created August 20, 2020 23:59
configure
# Compatibility config.h generated by the CMake build system
###############################################################################
# (1) Location of the installation
BASEDIR=/usr/local/amber20_src/build
AMBER_PREFIX=/usr/local/amber20//
BINDIR=$(AMBER_PREFIX)/bin
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pgbarletta / CMakeCache.txt
Created August 21, 2020 19:41
CMakeCache
# This is the CMakeCache file.
# For build in directory: /home/pbarletta/amber20_src/build
# It was generated by CMake: /usr/bin/cmake
# You can edit this file to change values found and used by cmake.
# If you do not want to change any of the values, simply exit the editor.
# If you do want to change a value, simply edit, save, and exit the editor.
# The syntax for the file is as follows:
# KEY:TYPE=VALUE
# KEY is the name of a variable in the cache.
# TYPE is a hint to GUIs for the type of VALUE, DO NOT EDIT TYPE!.
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pgbarletta / gist:4c5d8a540379ce5d321fad3c09470948
Created November 12, 2020 14:08
sample fixed with file
-6.9827E-03 -1.2060E-02 -3.3270E-03 5.5845E-03 -3.2249E-04 4.7521E-03 1.4404E-02 8.0357E-03 9.3137E-03 -9.2654E-03 5.0851E-03 -4.1534E-03 8.0331E-03 -1.8683E-02 -3.0116E-03 -1.7126E-02 4.6249E-03 4.3449E-04 3.4349E-03 4.7597E-03 -1.9952E-02 -1.4510E-02 1.9948E-02 -1.1514E-02 5.2085E-04 1.2077E-02 -2.7057E-03 6.2760E-03 -1.5432E-02 2.1348E-02
-1.0917E-02 -1.8234E-02 -1.0469E-02 1.2871E-03 -9.4562E-03 1.7884E-02 1.7945E-02 3.8684E-03 1.5073E-02 -6.8396E-03 1.7008E-02 5.2361E-03 7.9040E-03 -3.3773E-03 3.0501E-03 8.9497E-03 -1.7244E-03 -2.3878E-03 2.3819E-03 -1.0553E-02 1.9088E-02 -9.6169E-03 -2.7147E-03 -2.7411E-03 -4.7664E-03 9.2445E-05 -7.8470E-03 3.2568E-03 -1.0433E-02 -1.3052E-02
6.4556E-03 6.5247E-03 7.8063E-03 -8.7517E-03 -2.4766E-03 -7.2918E-04 -4.7568E-03 1.6271E-02 2.9609E-03 -9.9944E-03 1.6501E-02 3.1646E-03 5.3735E-03
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pgbarletta / gist:360040302c9874dc91b9356366f00c93
Created November 12, 2020 14:14
sample output
-6.9827E-03 -1.2060E-02 -3.3270E-03 5.5845E-03 -3.2249E-04 4.7521E-03 1.4404E-02 8.0357E-03 9.3137E-03 -9.2654E-03 5.0851E-03 -4.1534E-03 8.0331E-03 -1.8683E-02 -3.0116E-03 -1.7126E-02 4.6249E-03 4.3449E-04 3.4349E-03 4.7597E-03 -1.9952E-02 -1.4510E-02 1.9948E-02 -1.1514E-02 5.2085E-04 1.2077E-02 -2.7057E-03 6.2760E-03 -1.5432E-02 2.1348E-02
-1.0917E-02 -1.8234E-02 -1.0469E-02 1.2871E-03 -9.4562E-03 1.7884E-02 1.7945E-02 3.8684E-03 1.5073E-02 -6.8396E-03 1.7008E-02 5.2361E-03 7.9040E-03 -3.3773E-03 3.0501E-03 8.9497E-03 -1.7244E-03 -2.3878E-03 2.3819E-03 -1.0553E-02 1.9088E-02 -9.6169E-03 -2.7147E-03 -2.7411E-03 -4.7664E-03 9.2445E-05 -7.8470E-03 3.2568E-03 -1.0433E-02 -1.3052E-02
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pgbarletta / result.jl
Created July 19, 2021 22:00
struct Result
profile::Any
score::Any
end
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pgbarletta / a.pdb
Created June 14, 2022 14:14
biobb_model
ATOM 3242 N ALA B 1 49.830 33.030 25.480 1.00 0.00 N
ATOM 3243 H1 ALA B 1 50.530 32.320 25.620 1.00 0.00 H
ATOM 3244 H2 ALA B 1 49.230 32.900 24.680 1.00 0.00 H
ATOM 3245 H3 ALA B 1 50.280 33.940 25.390 1.00 0.00 H
ATOM 3246 CA ALA B 1 48.960 33.020 26.660 1.00 0.00 C
ATOM 3247 HA ALA B 1 49.210 32.120 27.230 1.00 0.00 H
ATOM 3248 CB ALA B 1 49.230 34.200 27.590 1.00 0.00 C
ATOM 3249 HB1 ALA B 1 48.530 34.040 28.410 1.00 0.00 H
ATOM 3250 HB2 ALA B 1 50.260 34.080 27.920 1.00 0.00 H
ATOM 3251 HB3 ALA B 1 49.060 35.140 27.080 1.00 0.00 H